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Re: SNES Problem



it again, the push and pop() functions dont seem to work, and they are
keeping me from compiling the program, this is the main timestep loop:



PETSC_ERR_ARG_DOMAIN didnt work:  error on line 6500 of SNESG3D2.F:
data type is undefined for variable PETSC_ERR_ARG_DOMAIN
Even thought I had petsc.h included.



  Is it just not compiling because  PETSC_ERR_ARG_DOMAIN is not
defined? Or does it still not work even when you have put the number in?
What is the error? Or did you get it all working with SNES?

  It may work automatically with TS; you would just set TS with a
smaller timestep and call TSSolve again?

  Barry

  I'm adding a petscerror.h for Fortran that includes these values
Sorry I forgot we hadn't given them for Fortran.

On Thu, 2 Mar 2006, Nils Erik Svangård wrote:




Hi again,
I realised that my implementation was a bit flawed so I have rewritten
it again, the push and pop() functions dont seem to work, and they are
keeping me from compiling the program, this is the main timestep loop:

     call VecCreateSeq(PETSC_COMM_SELF,N,x,ierr)
     call VecDuplicate(x,r,ierr)
     call VecDuplicate(x,xb,ierr)
     call SNESCreate(PETSC_COMM_SELF,snes,ierr)
     call SNESSetFunction(snes,r,FormFunction,PETSC_NULL_OBJECT,ierr)
     call SNESSetFromOptions(snes,ierr)
     call FormInitialGuess(x,ierr)
     call VecCopy(x,xb,ierr)
     write(6,*)zero,dt,tmax,i1000
     step=0
     timestep=dt
C While loop
  10 if (step .le. 100) then
       call PetscExceptionPush(87,ierr)
       call SNESSolve(snes,PETSC_NULL_OBJECT,x,ierr)
       call PetscExceptionPop(87,ierr2)

       call SNESGetConvergedReason(snes,reason,ierr)
       IF ( reason .LT. 0 ) THEN
          timestep=timestep/2
          VecCopy(xb,x,ierr)
          write(6,*)"Solution diverged, trying with",
    .               " smaller timestep: ",timestep
       ELSE
        IF ( ierr .EQ. 87) THEN
          timestep=timestep/2
          VecCopy(xb,x,ierr)
          write(6,*) "No physical solution, trying",
    .                " with smaller timestep: ",timestep
        ELSE
          timestep=dt
          step=step+1
          VecCopy(x,xb,ierr)
          write(6,*) "Solve success, going for step: ",step
        ENDIF
       ENDIF
      goto 10
     endif
C End While loop

And in my Formfunction I have added the following check:
if (ET(L) .LT. 0) then
               ierr = 87
               return
             endif

PETSC_ERR_ARG_DOMAIN didnt work:  error on line 6500 of SNESG3D2.F:
data type is undefined for variable PETSC_ERR_ARG_DOMAIN
Even thought I had petsc.h included.

Can I do this check when I use TS also? I have the sameproblem with
the values being negative when using TS.


/nisse


On 2/27/06, Barry Smith <bsmith@mcs.anl.gov> wrote:



   SNES works by computing p = -approxinv(J)*F(uold) and
then does a line search on unew = uold + lambda*p to get the
new u. First it uses a test value of 1 for lambda so it
tries to compute F(uold + p). It is possible that uold + p
has some "non-physical" values in it.  There are two ways
you can try handling it:

1) Before doing the linesearch SNES calls a "precheck" function,
that can change the step if it decides there is a problem
with the step (like it is too long). You can provide your
own precheck function with SNESLineSearchSetPreCheck() it could,
for example, shrink the Newton direction to make it remain physical.

or 2) when your form function detects an illegal value it calls
SETERRQ(PETSC_ERR_ARG_DOMAIN,"Nonphysical function input"); Note:
this is before it takes the square root of the negative number,
so check the number and call the error before calling SETERRQ().
(If using Fortran then simply set ierr = PETSC_ERR_ARG_DOMAIN and
then immediately return). Then replace your call to SNESSolve with
   ierr = PetscExceptionTry1(SNESSolve(snes,b,x),PETSC_ERR_ARG_DOMAIN);
   if (PetscExceptionCaught(ierr,PETSC_ERR_ARG_DOMAIN)) {
     /* this means your function found a non-physical value so
        cut your time-step and continue through the loop again. */
        Put code to do this here.
   }
If using fortran then do
call PetscExceptionPush(PETSC_ERR_ARG_DOMAIN,ierr)
call SNESSolve(snes,b,x,ierr)
call PetscExceptionPop(PETSC_ERR_ARG_DOMAIN,anotherierr)
if (ierr == PETSC_ERR_ARG_DOMAIN) then
   non-physical value so cut the time-step and try again
else ! everything is normal so take the next time-step

   Barry

The Fortran interface may be missing PetscExceptionPush() and Pop()
if so let us know and we'll provide the patch.

On Mon, 27 Feb 2006, Nils Erik Svangård wrote:




Hi all,

I have problems solving some CFD problems using SNES and my custom
back-euler. I have 7 equations that I want to solve.

First my FormFunction copies the values from the Vec that SNES uses to
the variables that my code use:

     RO(L)=xx(1,L)
     RU(L)=xx(2,L)
     RV(L)=xx(3,L)
     RW(L)=xx(4,L)
     ET(L)=xx(5,L)
     RQ(L)= xx(6,L)
     REPS(L)=xx(7,L)

Here I also print the values of ET(2) for debugging:

     write(6,*)"ET(2) = xx(5,2) : ",ET(2)," = ",xx(5,2)

Then I get the fluxes by calling custom functions

     call AUXVR
     call VGRAD
     call FLUX
     call KESRC

Then I perform back-euler  save the new value to so that I can use it
in the next iterationi (TSF(L) is Time step function, which is set by
hand and is the same for all L):

     ff(1,L) = RO(L)-OLD(1,L)-TSF(L)*DRO(L)
     ff(2,L) = RU(L)-OLD(2,L)-TSF(L)*DRU(L)
     ff(3,L) = RV(L)-OLD(3,L)-TSF(L)*DRV(L)
     ff(4,L) = RW(L)-OLD(4,L)-TSF(L)*DRW(L)
     ff(5,L) = ET(L)-OLD(5,L)-TSF(L)*DET(L)
     ff(6,L) = RQ(L)-OLD(6,L)-TSF(L)*DRQ(L)
     ff(7,L) = REPS(L)-OLD(7,L)-TSF(L)*DREPS(L)

And save the new value of RO-REPS to use in the next iteration of back-euler:

     OLD(1,L)=RO(L)
     OLD(2,L)=RU(L)
     OLD(3,L)=RV(L)
     OLD(4,L)=RW(L)
     OLD(5,L)=ET(L)
     OLD(6,L)=RQ(L)
     OLD(7,L)=REPS(L)

Here I print the values of L=2 as above for debugging:

     write(6,*)ff(5,2)," = ",ET(2),"-",OLD(5,2),"-",TSF(2),"*",DET(2)



The program exit abnormaly after 33 runs of the FormFunction. The
cause of this is that AUXVR tries to perform sqrt(ET(2)) when ET(2) is
negative, ET is the total energy and should never be negative. It
seems that all of a sudden the PETSc SNES solver decides to supply the
FormFunction with a negative ET value. I need help understanding why
and how to fix it (if it is fixable).

Here is the output of:
     write(6,*)"ET(2) = xx(5,2) : ",ET(2)," = ",xx(5,2)
Which is in the beginning of my FormFunction.
And:
     write(6,*)ff(5,2)," = ",ET(2),"-",OLD(5,2),"-",TSF(2),"*",DET(2)
Which is in the end of my Formfunction.

1. ET(2) = xx(5,2) :   253250.  =   253250.000000000
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
2. ET(2) = xx(5,2) :   253250.  =   253250.000010259
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
3. ET(2) = xx(5,2) :   253250.  =   253249.999999988
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4132419437260  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941324E+08
4. ET(2) = xx(5,2) :   253250.  =   253250.000048432
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
5. ET(2) = xx(5,2) :   253250.  =   253249.999999872
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4177283437784  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941773E+08
6. ET(2) = xx(5,2) :   253250.  =   253250.000071113
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
7. ET(2) = xx(5,2) :   253250.  =   253249.999980115
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4453347441010  =
253250. -  253250.000000000 -  1.000000E-07 * -2.944533E+08
8. ET(2) = xx(5,2) :   253250.  =   253250.000037298
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4082723436679  =
253250. -  253250.000000000 -  1.000000E-07 * -2.940827E+08
9. ET(2) = xx(5,2) :   253250.  =   253249.999942706
  ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4082723436679  =
253250. -  253250.000000000 -  1.000000E-07 * -2.940827E+08
10. ET(2) = xx(5,2) :   253250.  =   253249.999948703
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
11. ET(2) = xx(5,2) :   253250.  =   253250.000007808
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.7283811474088  =
253250. -  253250.000000000 -  1.000000E-07 * -2.972838E+08
12. ET(2) = xx(5,2) :   253250.  =   253250.000018146
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
13. ET(2) = xx(5,2) :   253250.  =   253250.000001865
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   28.3742819315846  =
253250. -  253250.000000000 -  1.000000E-07 * -2.837428E+08
14. ET(2) = xx(5,2) :   253250.  =   253249.999997296
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
15. ET(2) = xx(5,2) :   253250.  =   253250.000000049
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   30.6548963582361  =
253250. -  253250.000000000 -  1.000000E-07 * -3.065490E+08
16. ET(2) = xx(5,2) :   253250.  =   253250.000022870
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
17. ET(2) = xx(5,2) :   253250.  =   253249.999999716
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.5326051451209  =
253250. -  253250.000000000 -  1.000000E-07 * -2.953260E+08
18. ET(2) = xx(5,2) :   253250.  =   253250.000074328
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4165187437643  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941652E+08
19. ET(2) = xx(5,2) :   253250.  =   253250.000049809
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4085059436707  =
253250. -  253250.000000000 -  1.000000E-07 * -2.940851E+08
20. ET(2) = xx(5,2) :   253250.  =   253250.000019253
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
21. ET(2) = xx(5,2) :   253250.  =   253250.000000189
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.8851075492403  =
253250. -  253250.000000000 -  1.000000E-07 * -2.988511E+08
22. ET(2) = xx(5,2) :   253250.  =   253249.999997897
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4085059436707  =
253250. -  253250.000000000 -  1.000000E-07 * -2.940851E+08
23. ET(2) = xx(5,2) :   253250.  =   253249.999975142
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.3961539435263  =
253250. -  253250.000000000 -  1.000000E-07 * -2.939615E+08
24. ET(2) = xx(5,2) :   253250.  =   253250.000018324
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4085059436707  =
253250. -  253250.000000000 -  1.000000E-07 * -2.940851E+08
25. ET(2) = xx(5,2) :   253250.  =   253249.999987073
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4165187437643  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941652E+08
26. ET(2) = xx(5,2) :   253250.  =   253249.999980982
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4165187437643  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941652E+08
27. ET(2) = xx(5,2) :   253250.  =   253249.999994645
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
28. ET(2) = xx(5,2) :   253250.  =   253249.999962364
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4165187437643  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941652E+08
29. ET(2) = xx(5,2) :   253250.  =   253249.999999921
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
30. ET(2) = xx(5,2) :   253250.  =   253250.000000058
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   28.4019971319085  =
253250. -  253250.000000000 -  1.000000E-07 * -2.840200E+08
31. ET(2) = xx(5,2) :   253250.  =   253250.000040348
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4085059436707  =
253250. -  253250.000000000 -  1.000000E-07 * -2.940851E+08
32. ET(2) = xx(5,2) :   253250.  =   253250.000005245
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
33. ET(2) = xx(5,2) :   253250.  =   253250.000005245
   ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) :   29.4126563437192  =
253250. -  253250.000000000 -  1.000000E-07 * -2.941266E+08
34. ET(2) = xx(5,2) :  -848141.  =  -848141.388090847
--------------------------------------------------------------------------
Petsc Release Version 2.3.0, Patch 32, April, 26, 2005
See docs/changes/index.html for recent updates.
See docs/faq.html for hints about trouble shooting.
See docs/index.html for manual pages.
-----------------------------------------------------------------------
./SNESG3D2 on a linux-gnu named sethnx004.vac.com by yy26539 Mon Feb
27 14:21:13 2006
Libraries linked from /home/yy26539/work/NISSE/petsc-2.3.0/lib/linux-gnu
Configure run at Thu Oct 13 08:23:56 2005
Configure options --with-cc=gcc --with-fc="f77 -N109"
--download-mpich=1 --download-mpich-pm=gforker
--download-f-blas-lapack=1 --with-shared=0
-----------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 8 FPE: Floating Point
Exception,probably divide by zero
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------- Stack Frames ---------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:       INSTEAD the line number of the start of the function
[0]PETSC ERROR:       is given.
[0]PETSC ERROR: [0] SNES user function line 0 unknownunknown
[0]PETSC ERROR: [0] SNESComputeFunction line 788 src/snes/interface/snes.c
[0]PETSC ERROR: [0] SNESLineSearchCubic line 514 src/snes/impls/ls/ls.c
[0]PETSC ERROR: --------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:  !


Suggestions and tips are very welcome!
/nisse


--
Nils-Erik Svang�rd
MSN: schweingaard@hotmail.com
Skype: schweingaard








--
Nils-Erik Svangård
MSN: schweingaard@hotmail.com
Skype: schweingaard